scholarly journals Baculovirus: Molecular Insights on Their Diversity and Conservation

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Solange Ana Belen Miele ◽  
Matías Javier Garavaglia ◽  
Mariano Nicolás Belaich ◽  
Pablo Daniel Ghiringhelli
Keyword(s):  
Phylogenetic Analyses ◽  
Core Gene ◽  
Gene Sequences ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Large Group ◽  
Double Stranded Dna ◽  
Core Genes ◽  
Insect Viruses

The Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp. In this study, genome sequences from 57 baculoviruses were analyzed to reevaluate the number and identity of core genes and to understand the distribution of the remaining coding sequences. Thirty one core genes with orthologs in all genomes were identified along with other 895 genes differing in their degrees of representation among reported genomes. Many of these latter genes are common to well-defined lineages, whereas others are unique to one or a few of the viruses. Phylogenetic analyses based on core gene sequences and the gene composition of the genomes supported the current division of the Baculoviridae into 4 genera: Alphabaculovirus, Betabaculovirus, Gammabaculovirus, and Deltabaculovirus.

scholarly journals Complete Genome Sequences of Two Salmonella Viruses, VSe11 and VSe102 (Family Myoviridae, Subfamily Ounavirinae), with a Very High Degree of Similarity

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Egor A. Denisenko ◽  
Angelina A. Kislichkina ◽  
Vera P. Myakinina ◽  
Valentina M. Krasilnikova ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Complete Genome ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Content Type ◽  
Double Stranded Dna ◽  
Poultry Farms ◽  
High Degree ◽  
Degree Of Similarity ◽  
Very High

ABSTRACT Two lytic double-stranded DNA bacteriophages, VSe11 and VSe102, infecting broad-spectrum Salmonella enterica were isolated from the sewage of two different poultry farms. The phage genomes comprise 86,360 bp and 86,365 bp, respectively, with a G+C content of 39.0%, and both contain 129 putative coding sequences.

scholarly journals Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 925 ◽  
Author(s):  
Jiang Li ◽  
Xiaoyan Duan ◽  
Qianran Wang ◽  
Lei Zhang ◽  
Fei Deng ◽  
...  
Keyword(s):  
Southern China ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Viral Pathogen ◽  
Double Stranded Dna ◽  
Apoptosis Protein ◽  
Conserved Genes ◽  
Lepidopteran Pest ◽  
Core Genes

Artaxa digramma is a lepidopteran pest distributed throughout southern China, Myanmar, Indonesia, and India. Artaxa digramma nucleopolyhedrovirus (ArdiNPV) is a specific viral pathogen of A. digramma and deemed as a promising biocontrol agent against the pest. In this study, the complete genome sequence of ArdiNPV was determined by deep sequencing. The genome of ArdiNPV contains a double-stranded DNA (dsDNA) of 161,734 bp in length and 39.1% G+C content. Further, 149 hypothetical open reading frames (ORFs) were predicted to encode proteins >50 amino acids in length, covering 83% of the whole genome. Among these ORFs, 38 were baculovirus core genes, 22 were lepidopteran baculovirus conserved genes, and seven were unique to ArdiNPV, respectively. No typical baculoviral homologous regions (hrs) were identified in the genome. ArdiNPV had five multi-copy genes including baculovirus repeated ORFs (bros), calcium/sodium antiporter B (chaB), DNA binding protein (dbp), inhibitor of apoptosis protein (iap), and p26. Interestingly, phylogenetic analyses showed that ArdiNPV belonged to Clade II.b of Group II Alphabaculoviruses, which all contain a second copy of dbp. The genome of ArdiNPV was the closest to Euproctis pseudoconspersa nucleopolyhedrovirus, with 57.4% whole-genome similarity. Therefore, these results suggest that ArdiNPV is a novel baculovirus belonging to a newly identified cluster of Clade II.b Alphabaculoviruses.

scholarly journals Rhizobium lacunae sp. nov., Isolated From a Freshwater Pond

2021 ◽  
Author(s):  
Wen-Ming Chen ◽  
Che-Chia Yang ◽  
Chiu-Chung Young ◽  
Shih-Yao Lin ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Principal Fatty Acid ◽  
Freshwater Pond

Abstract Bacterial strain designated CSW-27T was isolated from a freshwater pond in Taiwan. Cells were Gram-stain-negative, aerobic, oxidase-positive, catalase-negative, rod-shaped and motile by flagella. Strain CSW-27T grew at 20-40 oC (optimum, 30-37 oC), at pH 5-9 (optimum, pH 6-7) and in the presence of 0-4% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set revealed that strain CSW-27T was affiliated with species in the genus Rhizobium. Analysis of 16S rRNA gene sequences showed that strain CSW-27T had the highest similarity to Rhizobium straminoryzae CC-LY845T (98.5%) followed by Rhizobium capsici CC-SKC2T (96.9%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CSW-27T and the closely related Rhizobium species were 73.4-86.5, 66.0-88.8 and 13.3-22.1%, respectively. The principal fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized aminophospholipid, three uncharacterized aminolipids and two uncharacterized lipids. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-27T was 63.3%. These polyphasic taxonomic data indicited that strain CSW-27T should be considered as representing a novel species in the genus Rhizobium, for which the name Rhizobium lacunae sp. nov. is proposed with strain CSW-27T (=BCRC 81244T =LMG 31684T) as the type strain.

scholarly journals Genomic Analysis of the Polyvalent Bacteriophage FP01

2019 ◽  
Author(s):  
Ignacio Vasquez ◽  
Julio Retamales ◽  
Barbara Parra ◽  
James Robeson ◽  
Javier Santander
Keyword(s):  
Escherichia Coli ◽  
Potential Application ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Host Factors ◽  
Coding Sequences ◽  
Double Stranded Dna ◽  
Host Infection ◽  
Lysogenic Phage

Recently the polyvalent bacteriophage FP01, isolated from wastewater in Valparaiso, Chile, was described to have lytic activity across species against Escherichia coli and Salmonella enterica serovars. Due to it polyvalent nature the bacteriophage FP01 could have potential application in food and agri-industry. Also, fundamental aspects of polyvalent bacteriophage biology are not well known. In this study we sequenced and describe the complete genome of the polyvalent phage FP01 (MH745368) using the nanopore technology. The bacteriophage FP01 genome has a 44,900 bp, double-stranded DNA with an average G+C content of 49.41% and 90 coding sequences (CDSs). We found that the phage FP01 critically depends on host factors for replication and transcription. Also, it has a critical lysogenic repressor pseudogene. Phylogenetic analyses indicated that the phage FP01 is closely related to phages lambda and P22. These results suggest that the phage FP01 could be a lytic variant of a lysogenic phage or acquired genes from lysogenic phages during host infection.

scholarly journals Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov.

2021 ◽  
Author(s):  
Berenice Talamantes-Becerra ◽  
Jason Carling ◽  
Jochen Blom ◽  
Arthur Georges
Keyword(s):  
New Genus ◽  
Gene Tree ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenetic Study ◽  
Genome Sequences ◽  
New Classification ◽  
Maximum Likelihood Tree ◽  
Average Amino Acid Identity ◽  
Core Genes

A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using publicly available whole genome sequences. A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment of a set of 662 orthologous core genes. The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus, and clade II, containing the majority of Anoxybacillus species. Clade I is further partitioned into three clades, consisting separately of Geobacillus, Parageobacillus, and a third clade which we suggest should be elevated to a new genus Quasigeobacillus gen. nov. Two species of Anoxybacillus showed inconsistent positioning among the trees produced by differing methods and could not be clearly resolved into any of the three existing genera or the new genus. This research shows the importance of considering closely related genera together when studying phylogeny or assigning genomic affinities.

scholarly journals Complete Genome Sequences of Three Siphoviridae Bacteriophages Infecting Salmonella enterica Serovar Enteritidis

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Rubina Paradiso ◽  
Serena Lombardi ◽  
Maria Grazia Iodice ◽  
Marita Georgia Riccardi ◽  
Massimiliano Orsini ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Complete Genome ◽  
Water Buffalo ◽  
Southern Italy ◽  
Lytic Activity ◽  
Genome Sequences ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Coding Sequences ◽  
Double Stranded Dna

Three bacteriophages, 118970_sal1, 118970_sal2, and 64795_sal3, were isolated from water buffalo feces in southern Italy, exhibiting lytic activity against Salmonella enterica serovar Enteritidis. These bacteriophages belong to the Siphoviridae family and have a 60,113-bp, 123,930-bp, and 48,094-bp double-stranded DNA (dsDNA) genome containing 72, 173, and 80 coding sequences (CDSs), respectively.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

scholarly journals Defining the Rhizobium leguminosarum Species Complex

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 111 ◽  
Author(s):  
J. Peter W. Young ◽  
Sara Moeskjær ◽  
Alexey Afonin ◽  
Praveen Rahi ◽  
Marta Maluk ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Species Complex ◽  
Rhizobium Leguminosarum ◽  
Housekeeping Genes ◽  
Single Species ◽  
Natural Unit ◽  
Genome Sequences ◽  
Distinct Entity ◽  
Type Strains ◽  
Core Genes

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

Phylogenetic analyses of some genera in Oedipodidae (Orthoptera: Acridoidea) based on 16S mitochondrial partial gene sequences

2008 ◽  
Vol 15 (5) ◽  
pp. 471-476 ◽  
Author(s):  
Xiang-Chu Yin ◽  
Xin-Jiang Li ◽  
Wen-Qiang Wang ◽  
Hong Yin ◽  
Cheng-Quan Cao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Sequences

scholarly journals Complete Genome Sequence of a Lytic Siphoviridae Bacteriophage Infecting Several Serovars of Salmonella enterica

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Rubina Paradiso ◽  
Serena Lombardi ◽  
Maria Grazia Iodice ◽  
Marita Georgia Riccardi ◽  
Massimiliano Orsini ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Water Buffalo ◽  
Southern Italy ◽  
Lytic Activity ◽  
Coding Sequences ◽  
Double Stranded Dna

The bacteriophage 100268_sal2 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against several subspecies of Salmonella enterica . This bacteriophage belongs to the Siphoviridae family and has a 125,114-bp double-stranded DNA (ds-DNA) genome containing 188 coding sequences (CDSs).

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